PSB 2020 Online Proceedings

PSB 2020
CC BY: PSB 2020 proceedings are published as Open Access chapters by World Scientific Publishing Company and distributed under the terms of the Creative Commons Attribution (CC BY) 4.0 License.

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Session Introduction
Roxana Daneshjou, Lukasz Kidzinski, Olga Afanasiev, Jonathan H. Chen; Pacific Symposium on Biocomputing 25:1-6(2020)
Predicting Longitudinal Outcomes of Alzheimer's Disease via a Tensor-Based Joint Classification and Regression Model
Lodewijk Brand, Kai Nichols, Hua Wang, Heng Huang, Li Shen, for the ADNI; Pacific Symposium on Biocomputing 25:7-18(2020)
Robustly Extracting Medical Knowledge from EHRs: A Case Study of Learning a Health Knowledge Graph
Irene Y. Chen, Monica Agrawal, Steven Horng, David Sontag; Pacific Symposium on Biocomputing 25:19-30(2020)
Increasing Clinical Trial Accrual via Automated Matching of Biomarker Criteria
Jessica W. Chen, Christian A. Kunder, Nam Bui, James L. Zehnder, Helio A. Costa, Henning Stehr; Pacific Symposium on Biocomputing 25:31-42(2020)
Addressing the Credit Assignment Problem in Treatment Outcome Prediction Using Temporal Difference Learning
Sahar Harati, Andrea Crowell, Helen Mayberg, Shamim Nema; Pacific Symposium on Biocomputing 25:43-54(2020)
Multiclass Disease Classification from Microbial Whole-Community Metagenomes
Saad Khan, Libusha Kelly; Pacific Symposium on Biocomputing 25:55-66(2020)
LitGen: Genetic Literature Recommendation Guided by Human Explanations
Allen Nie, Arturo L. Pineda, Matt W. Wright, Hannah Wand, Bryan Wulf, Helio A. Costa, Ronak Y. Patel, Carlos D. Bustamante, James Zou; Pacific Symposium on Biocomputing 25:67-78(2020)
From Genome to Phenome: Predicting Multiple Cancer Phenotypes Based on Somatic Genomic Alterations via the Genomic Impact Transformer
Yifeng Tao, Chunhui Cai, William W. Cohen, Xinghua Lu; Pacific Symposium on Biocomputing 25:79-90(2020)
Automated Phenotyping of Patients with Non-Alcoholic Fatty Liver Disease Reveals Clinically Relevant Disease Subtypes
Maxence Vandromme, Tomi Jun, Ponni Perumalswami, Joel T. Dudley, Andrea Branch, Li Li; Pacific Symposium on Biocomputing 25:91-102(2020)
Monitoring ICU Mortality Risk with a Long Short-Term Memory Recurrent Neural Network
Ke Yu, Mingda Zhang, Tianyi Cui, Milos Hauskrecht; Pacific Symposium on Biocomputing 25:103-114(2020)
Multilevel Self-Attention Model and Its Use on Medical Risk Prediction
Xianlong Zeng, Yunyi Feng, Soheil Moosavinasab, Deborah Lin, Simon Lin, Chang Liu; Pacific Symposium on Biocomputing 25:115-126(2020)
Identifying Transitional High Cost Users from Unstructured Patient Profiles Written by Primary Care Physicians
Haoran Zhang, Elisa Candido, Andrew S. Wilton, Raquel Duchen, Liisa Jaakkimainen, Walter Wodchis, Quaid Morris; Pacific Symposium on Biocomputing 25:127-138(2020)
Obtaining Dual-Energy Computed Tomography (CT) Information from a Single-Energy CT Image for Quantitative Imaging Analysis of Living Subjects by Using Deep Learning
Wei Zhao, Tianling Lv, Rena Lee, Yang Chen, Lei Xing; Pacific Symposium on Biocomputing 25:139-148(2020)


Session Introduction
Lukasz Kurgan, Predrag Radivojac, Joel L. Sussman, A. Keith Dunker; Pacific Symposium on Biocomputing 25:149-158(2020)
Many-to-One Binding by Intrinsically Disordered Protein Regions
Wei-Lun Alterovitz, Eshel Faraggi, Christopher J. Oldfield, Jingwei Meng, Bin Xue, Fei Huang, Pedro Romero, Andrzej Kloczkowski, Vladimir N. Uversky, A. Keith Dunker; Pacific Symposium on Biocomputing 25:159-170(2020)
Disordered Function Conjunction: On the In-Silico Function Annotation of Intrinsically Disordered Regions
Sina Ghadermarzi, Akila Katuwawala, Christopher J. Oldfield, Amita Barik, Lukasz Kurgan; Pacific Symposium on Biocomputing 25:171-182(2020)
De novo Ensemble Modeling Suggests that AP2-Binding to Disordered Regions Can Increase Steric Volume of Epsin but Not Eps15
N. Suhas Jagannathan, Christopher W. V. Hogue, Lisa Tucker-Kellogg; Pacific Symposium on Biocomputing 25:183-194(2020)
Modulation of p53 Transactivation Domain Conformations by Ligand Binding and Cancer-Associated Mutations
Xiaorong Liu, Jianhan Chen; Pacific Symposium on Biocomputing 25:195-206(2020)
Exploring Relationships Between the Density of Charged Tracts Within Disordered Regions and Phase Separation
Ramiz Somjee, Diana M. Mitrea, Richard W. Kriwacki; Pacific Symposium on Biocomputing 25:207-218(2020)


Session Introduction
Max D.M. Leiserson, Teresa M. Przytycka, Roded Sharan; Pacific Symposium on Biocomputing 25:219-225(2020)
PhySigs: Phylogenetic Inference of Mutational Signature Dynamics
Sarah Christensen, Mark D.M. Leiserson, Mohammed El-Kebir; Pacific Symposium on Biocomputing 25:226-237(2020)
TrackSigFreq: Subclonal Reconstructions Based on Mutation Signatures and Allele Frequencies
Caitlin F Harrigan, Yulia Rubanova, Quaid Morris, Alina Selega; Pacific Symposium on Biocomputing 25:238-249(2020)
Impact of Mutational Signatures on microRNA and Their Response Elements
Eirini Stamoulakatou, Pietro Pinoli, Stefano Ceri, Rosario Piro; Pacific Symposium on Biocomputing 25:250-261(2020)
DNA Repair Footprint Uncovers Contribution of DNA Repair Mechanism to Mutational Signatures
Damian Wojtowicz, Mark D.M. Leiserson, Roded Sharan, Teresa M. Przytycka; Pacific Symposium on Biocomputing 25:262-273(2020)
Genome Gerrymandering: Optimal Division of the Genome into Regions with Cancer Type Specific Differences in Mutation Rates
Adamo Young, Jacob Chmura, Yoonsik Park, Quaid Morris, Gurnit Atwal; Pacific Symposium on Biocomputing 25:274-285(2020)


Session Introduction
Shilpa Nadimpalli Kobren, Brett Beaulieu-Jones, Christian Darabos, Dokyoon Kim, Anurag Verma; Pacific Symposium on Biocomputing 25:286-294(2020)
Clinical Concept Embeddings Learned from Massive Sources of Multimodal Medical Data
Andrew L. Beam, Benjamin Kompa, Allen Schmaltz, Inbar Fried, Griffin Weber, Nathan Palmer, Xu Shi, Tianxi Cai, Isaac S. Kohane; Pacific Symposium on Biocomputing 25:295-306(2020)
Assessment of Imputation Methods for Missing Gene Expression Data in Meta-Analysis of Distinct Cohorts of Tuberculosis Patients
Carly A. Bobak, Lauren McDonnell, Matthew D. Nemesure, Justin Lin, Jane E. Hill; Pacific Symposium on Biocomputing 25:307-318(2020)
Towards Identifying Drug Side Effects from Social Media Using Active Learning and Crowd Sourcing
Sophie Burkhardt, Julia Siekiera, Josua Glodde, Miguel A. Andrade-Navarro, Stefan Kramer; Pacific Symposium on Biocomputing 25:319-330(2020)
Microvascular Dynamics from 4D Microscopy Using Temporal Segmentation
Shir Gur, Lior Wolf, Lior Golgher, Pablo Blinder; Pacific Symposium on Biocomputing 25:331-342(2020)
Using Transcriptional Signatures to Find Cancer Drivers with LURE
David Haan, Ruikang Tao, Verena Friedl, Ioannis N Anastopoulos, Christopher K Wong, Alana S Weinstein, Joshua M Stuart; Pacific Symposium on Biocomputing 25:343-354(2020)
PAGE-Net: Interpretable and Integrative Deep Learning for Survival Analysis Using Histopathological Images and Genomic Data
Jie Hao, Sai Chandra Kosaraju, Nelson Zange Tsaku, Dae Hyun Song, Mingon Kang; Pacific Symposium on Biocomputing 25:355-366(2020)
Machine Learning Algorithms for Simultaneous Supervised Detection of Peaks in Multiple Samples and Cell Types
Toby Dylan Hocking, Guillaume Bourque; Pacific Symposium on Biocomputing 25:367-378(2020)
Learning a Latent Space of Highly Multidimensional Cancer Data
Benjamin Kompa, Beau Coker; Pacific Symposium on Biocomputing 25:379-390(2020)
Scaling Structural Learning with NO-BEARS to Infer Causal Transcriptome Networks
Hao-Chih Lee, Matteo Danieletto, Riccardo Miotto, Sarah T. Cherng, and Joel T. Dudley; Pacific Symposium on Biocomputing 25:391-402(2020)
PathFlowAI: A High-Throughput Workflow for Preprocessing, Deep Learning and Interpretation in Digital Pathology
Joshua J. Levy, Lucas A. Salas, Brock C. Christensen, Aravindhan Sriharan, Louis J. Vaickus; Pacific Symposium on Biocomputing 25:403-414(2020)
Improving Survival Prediction Using a Novel Feature Selection and Feature Reduction Framework Based on the Integration of Clinical and Molecular Data
Lisa Neums, Richard Meier, Devin C. Koestler, Jeffrey A. Thompson; Pacific Symposium on Biocomputing 25:415-426(2020)
Bayesian Semi-Nonnegative Matrix Tri-Factorization to Identify Pathways Associated with Cancer Phenotypes
Sunho Park, Nabhonil Kar, Jae-Ho Cheong, Tae Hyun Hwang; Pacific Symposium on Biocomputing 25:427-438(2020)
Graph-Based Information Diffusion Method for Prioritizing Functionally Related Genes in Protein- Protein Interaction Networks
Minh Pham, Olivier Lichtarge; Pacific Symposium on Biocomputing 25:439-450(2020)
Tree-Weighting for Multi-Study Ensemble Learners
Maya Ramchandran, Prasad Patil, Giovanni Parmigiani; Pacific Symposium on Biocomputing 25:451-462(2020)
A Literature-Based Knowledge Graph Embedding Method for Identifying Drug Repurposing Opportunities in Rare Diseases
Daniel N. Sosa, Alexander Derry, Margaret Guo, Eric Wei, Connor Brinton, Russ B. Altman; Pacific Symposium on Biocomputing 25:463-474(2020)
PTR Explorer: An approach to identify and explore Post Transcriptional Regulatory mechanisms using proteogenomics
Arunima Srivastava, Michael Sharpnack, Kun Huang, Parag Mallick, Raghu Machiraju Dowell; Pacific Symposium on Biocomputing 25:475-486(2020)
Two-stage ML Classifier for Identifying Host Protein Targets of the Dengue Protease
Jacob T. Stanley, Alison R. Gilchrist, Alex C. Stabell, Mary A. Allen, Sara L. Sawyer, Robin D. Dowell; Pacific Symposium on Biocomputing 25:487-498(2020)
Network Representation of Large-Scale Heterogeneous RNA Sequences with Integration of Diverse Multi-omics, Interactions, and Annotations Data
Nhat Tran, Jean Gao; Pacific Symposium on Biocomputing 25:499-510(2020)
Enhancing Model Interpretability and Accuracy for Disease Progression Prediction via Phenotype-Based Patient Similarity Learning
Yue Wang, Tong Wu, Yunlong Wang, Gao Wang; Pacific Symposium on Biocomputing 25:511-522(2020)
Hadoop and PySpark for Reproducibility and Scalability of Genomic Sequencing Studies
Nicholas R. Wheeler, Penelope Benchek, Brian W. Kunkle, Kara L. Hamilton-Nelson, Mike Warfe, Jeremy R. Fondran, Jonathan L. Haines, William S. Bush; Pacific Symposium on Biocomputing 25:523-534(2020)
CERENKOV3: Clustering and Molecular Network-Derived Features Improve Computational Prediction of Functional Noncoding SNPs
Yao Yao, Stephen A. Ramsey; Pacific Symposium on Biocomputing 25:535-546(2020)


Session Introduction
Steven E. Brenner, Martha L. Bulyk, Dana C. Crawford, Alexander A. Morgan, Predrag Radivojac, Nicholas P. Tatonetti; Pacific Symposium on Biocomputing 25:547-550(2020)
Integrated Cancer Subtyping using Heterogeneous Genome-Scale Molecular Datasets
Suzan Arslanturk, Sorin Draghici, Tin Nguyen; Pacific Symposium on Biocomputing 25:551-562(2020)
AnomiGAN: Generative Adversarial Networks for Anonymizing Private Medical Data
Ho Bae, Dahuin Jung, Hyun-Soo Choi, Sungroh Yoon; Pacific Symposium on Biocomputing 25:563-574(2020)
Frequency of ClinVar Pathogenic Variants in Chronic Kidney Disease Patients Surveyed for Return of Research Results at a Cleveland Public Hospital
Dana C. Crawford, John Lin, Jessica N. Cooke Bailey, Tyler Kinzy, John R. Sedor, John F. O'Toole, Williams S. Bush; Pacific Symposium on Biocomputing 25:575-586(2020)
Assessment of Coverage for Endogenous Metabolites and Exogenous Chemical Compounds Using an Untargeted Metabolomics Platform
Sek Won Kong, Carles Hernandez-Ferrer; Pacific Symposium on Biocomputing 25:587-598(2020)
Coverage Profile Correction of Shallow-Depth Circulating Cell-Free DNA Sequencing via Multi- Distance Learning
Nicholas B. Larson, Melissa C. Larson, Jie Na, Carlos P. Sosa, Chen Wang, Jean-Pierre Kocher, Ross Rowsey; Pacific Symposium on Biocomputing 25:599-610(2020)
PGxMine: Text Mining for Curation of PharmGKB
Jake Lever, Julia M. Barbarino, Li Gong, Rachel Huddart, Katrin Sangkuhl, Ryan Whaley, Michelle Whirl-Carrillo, Mark Woon, Teri E. Klein and Russ B. Altman; Pacific Symposium on Biocomputing 25:611-622(2020)
Network-Based Matching of Patients and Targeted Therapies for Precision Oncology
Qingzhi Liu, Min Jin Ha, Rupam Bhattacharyya, Lana Garmire, Veerabhadran Baladandayuthapani; Pacific Symposium on Biocomputing 25:623-634(2020)
The Power of Dynamic Social Networks to Predict Individuals' Mental Health
Shikang Liu, David Hachen, Omar Lizardo, Christian Poellabauer, Aaron Striegel, Tijana Milenkovic; Pacific Symposium on Biocomputing 25:635-646(2020)
Implementing a Cloud Based Method for Protected Clinical Trial Data Sharing
Gaurav Luthria, Qingbo Wang; Pacific Symposium on Biocomputing 25:647-658(2020)
Phenome-wide Association Studies on Cardiovascular Health and Fatty Acids Considering Phenotype Quality Control Practices for Epidemiological Data
Kristin Passero, Xi He, Jiayan Zhou, Bertram Mueller-Myhsok, Marcus E. Kleber, Winfried Maerz, Molly A. Hall; Pacific Symposium on Biocomputing 25:659-670(2020)
Pathway and Network Embedding Methods for Prioritizing Psychiatric Drugs
Yash Pershad, Margaret Guo, Russ B. Altman; Pacific Symposium on Biocomputing 25:671-682(2020)
aTEMPO: Pathway-Specific Temporal Anomalies for Precision Therapeutics
Christopher Michael Pietras, Liam Power, Donna K. Slonim; Pacific Symposium on Biocomputing 25:683-694(2020)
Robust-ODAL: Learning from Heterogeneous Health Systems Without Sharing Patient-Level Data
Jiayi Tong, Rui Duan, Ruowang Li, Martijn J. Scheuemie, Jason H. Moore, Yong Chen; Pacific Symposium on Biocomputing 25:695-706(2020)
Feature Selection and Dimension Reduction of Social Autism Data
Peter Washington, Kelley Marie Paskov, Haik Kalantarian, Nathaniel Stockham, Catalin Voss, Aaron Kline, Ritik Patnaik, Brianna Chrisman, Maya Varma, Qandeel Tariq, Kaitlyn Dunlap, Jessey Schwartz, Nick Haber, Dennis P. Wall; Pacific Symposium on Biocomputing 25:707-718(2020)
Computationally Efficient, Exact, Covariate-Adjusted Genetic Principal Component Analysis by Leveraging Individual Marker Summary Statistics from Large Biobanks
Jack Wolf, Martha Barnard, Xueting Xia, Nathan Ryder, Jason Westra, Nathan Tintle; Pacific Symposium on Biocomputing 25:719-730(2020)


AI Ethics and Values in Biomedicine – Technical Challenges and Solutions
Dragutin Petkovic, Lester Kobzik, Reza Ghanadan; Pacific Symposium on Biocomputing 25:731-735(2020)
Navigating Ethical Quandaries with the Privacy Dilemma of Biomedical Datasets
Gamze Gursoy, Megan Doerr, John Wilbanks, Jennifer K. Wagner, Haixu Tang, Steven E. Brenner; Pacific Symposium on Biocomputing 25:736-738(2020)
Packaging Biocomputing Software to Maximize Distribution and Reuse
William S. Bush, Nicholas Wheeler, Brett Beaulieu-Jones, Christian Darabos; Pacific Symposium on Biocomputing 25:739-742(2020)
Translational Bioinformatics: Biobanks in the Precision Medicine Era
Marylyn Ritchie, Jason Moore, Ju Han Kim; Pacific Symposium on Biocomputing 25:743-747(2020)

Funding for this conference was made possible (in part) by Grant # 5 R13 LM006766 from the National Library of Medicine. The views expressed in written conference materials or publications, and by speakers and moderators, does not necessarily reflect the official policies of the Department of Health and Human Services; nor does mention by trade names, commercial practices, or organizations imply endorsement by the U.S. Government.

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